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Molecular and Cellular Biology, November 2007, p. 7865-7870, Vol. 27, No. 22
0270-7306/07/$08.00+0 doi:10.1128/MCB.00397-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.
,
Huiping Ling,1
Edwin R. Smith,2,
and
John C. Lucchesi1*
Department of Biology,1 Department of Cell Biology, Emory University, Atlanta, Georgia 303222
Received 6 March 2007/ Returned for modification 10 April 2007/ Accepted 31 August 2007
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To facilitate the study of the mechanism underlying dosage compensation, we developed an experimental model by reproducing dosage compensation on a plasmid transfected and expressed transiently in cultured cells. This model represents a level of biological complexity that is intermediate between in vitro reconstitutions and chromatin extracted from embryos or other developmental stages. It is substantially more amenable to biochemical manipulations than experimental material from larval salivary glands, and the possibility of using RNA interference (RNAi) offsets the use of mutations. Lastly, because the compensated element is a circular DNA plasmid, it allows the study of topological changes that underlie the compensation process.
The function of the MSL complex is unlikely to be the initiation of gene activity. This conclusion derives from the observation that X-linked genes are activated in normal spatial and temporal fashions in wild-type females, where the complex is absent, and in mutant males, where the complex is inactive (in mutant males, X-linked gene products are present at half the normal level, eventually leading to lethality). Furthermore, the acetylation of H4K16 does not favor the promoter region of compensated genes; it occurs throughout transcriptional units, and its level actually tends to increase towards the 3' end (24). The distribution of H4K16ac in X-linked transcriptional domains, coupled with the observation that dosage-compensated genes exhibit an approximately twofold enhancement in steady-state levels of product irrespective of the strengths of their promoters, has led to the conclusion that the primary mechanistic result of the chromatin modifications responsible for dosage compensation is an enhancement in the rate of transcription elongation (24), i.e., an increase in the extension rate of the RNA polymerase. This conclusion was supported recently by Alekseyenko et al. (2) and Gilfillan et al. (7), who used chromatin immunoprecipitation (ChIP) with high-resolution microarrays to map the position of the MSL complex along the X chromosome.
We used the plasmid model to ask whether the rate of elongation of RNA polymerase II (RNAP II) on compensated genes depends on the presence of histone modifications associated with active genes and laid down by the process of transcription by testing the effect of the loss of several known marks and factors associated with the elongation function of RNAP II. We observed that the relative increase in the rate of transcription of dosage-compensated chromatin is not affected by a reduction in the levels of the histone methyltransferases Set1, Set2, or Mes-4 or of the PAF1 and FACT complexes but is affected by reducing the level of MOF. These observations emphasize the unique role played by acetylated H4K16 in this process.
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S2 transfection and transcription assays. Drosophila Schneider line 2 (S2) cells were grown in HyQ SFX-insect medium (HyClone) with penicillin-streptomycin antibiotic at 25oC without CO2. Cells were split 2 to 22 h prior to transfection to 30 to 60% confluence. Transfection was carried out following the QIAGEN Effectene protocol with 1.0 ng ptTA plasmid, 5.4 ng R plasmid, 1.2 µg pBluescript (Stratagene), and 15 ng supercoiled (or 30 ng relaxed) FF, roX2-FF, N-FF plasmid, or 100 ng of Mtn-Sxl plasmid, 10.8 µl enhancer, and 19.2 µl Effectene reagent for 5 x 106 cells. On the next day, the cells were split to a final concentration of 0.3 x 106 cells/ml. Three to 5 days after transfection, the cells were collected for the luciferase assay, RNA isolation, DNA isolation, and/or protein isolation. Luciferase activity was determined by using the dual luciferase reporter assay system (Promega). The firefly luciferase activity was normalized to Renilla luciferase activity for each sample. At least three independent experiments were performed; error bars in the figures represent standard deviations of the means.
ChIP analysis. Chromatin from transfected S2 cells was immunoprecipitated following the method of Oberley and Farnham (18), with the following modifications. Sonication was performed with 25 sets of 4-s pulses; preclearing was performed with protein A-coated beads treated with tRNA, salmon sperm, and bovine serum albumin; and cross-linking was reversed at 65°C in 0.2 M NaCl. ChIP grade H4K16ac and H3K36me3 antisera were purchased from Serotec and Abcam, respectively; RFX antiserum, a gift of J. Boss, was used as a background immunoprecipitation control; the supernatant was used as input. DNA was isolated with a QIAquick PCR purification kit (QIAGEN). The level of pull down of the firefly luciferase gene was measured by quantitative PCR with a pair of primers spanning an internal region in the case of H4K16ac and with three pairs of primers spanning 5', internal, and 3' regions in the case of H3K36me3 (see Table S1A in the supplemental material for primer sequences).
RNAi knockdown.
The day before transfection, 0.9 x106 S2 cells were transferred to a six-well culture dish 3 to 5 h prior to pretreatment with 10 µg/ml double-stranded RNA (dsRNA). Cells were transfected 18 to 22 h later and, 1 day after transfection, were split to
0.3 x 106 cells/ml. Additional dsRNA was added to the medium at that time to maintain the 10 µg/ml concentration. dsRNA was made following Ambion's MEGAscript protocol. The primers used to amplify the 500- to 600-bp regions of the dSet1, dSet2, Mes-4, dSsrp, dSpt16, mof, msl2, and green fluorescent protein (GFP) genes are presented in Table S1B in the supplemental material.
Immunoblot analysis. Protein extracts were isolated from S2 cell pellets in Laemmli sample buffer, separated on Criterion Tris-HCl gels (Bio-Rad) and transferred to a polyvinylidene difluoride membrane by using 20% methanol-Tris-glycine transfer buffer, following Bio-Rad's Criterion protocol. Primary antibodies used were H3 (1:5,000, Abcam), H3K4me1 (Abcam; 1:500), H3K4me2 (Upstate; 1:2,000), H3K4me3 (Abcam; 1:2,000), H3K36me1 (Abcam; 1:1,000), H3K36me2 (Upstate catalog no. 07-369, 1:2,000), H3K36me3 (Abcam; 1:2,000), and Drosophila FACT subunits dSPT16 and dSSRP1 (received from S. Hirose [22]; 1:5,000). After secondary anti-rabbit horseradish peroxidase antibody labeling (Pierce; 1:20,000), immunoblots were developed by using enhanced chemiluminescence (ECL-Plus; GE Healthcare) and quantitated with a Bio-Rad Fluor-S Multi-Imager Max or ImageJ program on scanned developed films. The levels of knockdown expressed as a percentage of control (GFP RNAi) are listed in Table S2 in the supplemental material.
Quantitative RT-PCR. Total RNA was isolated using the QIAGEN RNeasy kit. Real-time reverse transcription-PCR (RT-PCR) measurements of the levels of firefly, Renilla, ribosomal protein 49 (RP49), glucose-6-phosphate dehydrogenase (G6PD), 6-phosphogluconate dehydrogenase (6PGD), dSpt6, glycerol 3-phosphate dehydrogenase (GPDH), and dSpt4 transcripts were made using the QIAGEN QuantiTect SYBR green RT-PCR kit and the Bio-Rad iCycler. For the gene-specific primer pairs, see Table S1C in the supplemental material. The level of transcripts from each gene was normalized to the internal standard RP49. The number of normalized cycles of the compensated GFP-treated sample was set to 1, and the percentage of change from that number is plotted as the relative level of mRNA. Error bars represent standard deviations from the means of at least three different treatments/transfections.
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FIG. 1. The plasmid model of dosage compensation. (A) Diagram of the plasmids used to transfect S2 cells. The FF plasmid contains tetO inserted upstream of the firefly luciferase gene; the roX-FF plasmid includes the roX2 gene sequence downstream of the firefly luciferase gene; the R plasmid contains the Renilla luciferase gene under the control of the copia promoter; the ptTA plasmid expresses the tTA transcriptional activator gene driven by the alpha-tubulin promoter. Experimental (right panel) and control (left panel) transfections are indicated. (B) Southern blots of DNA extracted from S2 cells at 4 days posttransfection run in agarose gels with two different concentrations of chloroquine and probed with a firefly luciferase sequence. X and N refer to roX-FF and N-FF plasmids, respectively (see Materials and Methods). (C) There is a twofold enhancement in firefly luciferase relative to Renilla luciferase activity due to the presence of the roX sequence in the absence of tTA because the tetO promoter exhibits some leakiness; the twofold difference is maintained over a wide range of cotransfection with the tTA-expressing plasmid. (D) The enhancement is abrogated by the presence of an SXL-expressing plasmid under the control of the Drosophila metallothionein promoter (left panel) or by RNAi to deplete MSL2 (right panel). GFP denotes an RNAi control with GFP dsRNA. (E) ChIP analysis reveals a better than 10-fold enrichment in H4K16ac on the roX2-bearing plasmid that is eliminated by cotransfection with SXL. Each experiment was repeated three times, and the error bars represent the standard deviations of the means (the experiment for panel D, left side, was performed twice).
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All of the evidence available to date leads to the conclusion that the MSL complex does not play a role in X-linked gene activation; rather, it modifies the chromatin organization of activated genes in order to enhance the level of their transcription. As noted above (Fig. 1D), depletion of the MSL complex by cotransfection with a Sxl-expressing plasmid or by RNAi targeted to the MSL2 subunit eliminates the transcriptional enhancement exhibited by the roX-bearing plasmid. This effect is thought to result from the absence of H4K16 acetylation. We tested this conclusion directly by RNAi depletion of MOF and observed that the level of dosage compensation of GFP-dsRNA-treated cells was reduced from 2.0 ± 0.07 to 1.44 ± 0.15 (n = 3). We used RNAi to test whether other histone marks found downstream of the promoter region of transcribed genes play a role in enhancing the rate of RNAP II elongation responsible for dosage compensation. We treated S2 cells with dsRNA homologous to CG1716, the Drosophila ortholog of yeast (Saccharomyces cerevisiae) SET2 that is responsible for the di- and trimethylation of H3K36, or CG40351, the Drosophila ortholog of yeast SET1 that is responsible for the di- and trimethylation of H3K4. We also depleted cells of PAF1 that is involved in the methylation of H3 at residues K4 and K79 and has been shown to interact physically with FACT in yeast. In Drosophila, PAF1 depletion diminishes the level of H3K4me3 greatly but has no effect on the di- or trimethylation of H3K79; in addition, the depletion of PAF1 results in significantly lower levels of FACT and Spt6 (1). Therefore, in order to parse the effects of depleting PAF1 on methylation and on the association of FACT with the transcript elongation complex, we targeted FACT specifically for RNAi. We used the plasmid system to assess the effects of all of these treatments on the mechanism of dosage compensation.
RNAi targeting of dSet1 or Paf1 reduced the level of H3K4me3 significantly in bulk chromatin without affecting the process of dosage compensation (Fig. 2A). Similar results were obtained by depleting dSET2, resulting in the overall decrease in the level of H3K36me3, with a concomitant increase in H3K36me2 (Fig. 2B). We then searched the Drosophila database for additional homologs of dSet2 and discovered Mes-4. A histone methyltransferase with the same name exists in Caenorhabditis elegans, where it was shown to be responsible for dimethylated H3K36 (3). RNAi depletion of this enzyme in S2 cells substantially reduced the level of H3K36me2 without any significant effect on H3K36me3. Once again, there was no effect on dosage compensation by the depletion of MES-4 alone (FIG. 2C) or in combination with the depletion of dSET2 (see Fig. S3 in the supplemental material). Lastly, we achieved the depletion of FACT by using RNAi against the genes encoding its two subunits dSpt16 and dSsrp. Surprisingly, the depletion of either subunit resulted in the depletion of the other, suggesting that they depend on their association for stability. Once again, we noted no effect on dosage compensation (Fig. 2D).
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FIG. 2. RNAi-mediated depletion of selected transcription-associated histone marks. (A) Treatment with dSet1 or Paf1 dsRNA reduces the level of nuclear H3K4me3 (upper panels) but has no effect on dosage compensation (lower panels). This is evidenced by the approximate twofold increase in relative firefly to Renilla luciferase expression by the roX-bearing plasmid (white columns) relative to the control plasmid (gray columns). Similar results are obtained by reducing the levels of H3K36me3 (B) or of H3K36me2 (C) by RNAi of dSet2 or Mes-4, respectively. (D) Knockdown of the Ssrp or Spt16 subunits of the FACT complex has no effect on dosage compensation. Each experiment was repeated three times, and the error bars represent the standard deviations of the means. X and N refer to the roX-FF and N-FF (control) plasmids, respectively.
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To establish that the results obtained with the plasmid system are an accurate reflection of the activity of endogenous chromosomal genes, we monitored the effects of dSET1, dSET2, and MES-4 depletion on the transcriptional activity level of three X-linked genes known to be dosage compensated. As a control, we measured the effect of knocking down the MSL complex on the same genes and on two autosomal genes that are not dosage compensated. The steady-state levels of transcripts of the X-linked Pgd, Zw, and Spt6 genes (encoding 6PGD, G6PD, and the Drosophila homologue of yeast suppressor of Ty6 [dSPT6], respectively), as measured by real-time RT-PCR, confirm our previous observation that the depletion of these three histone methyltransferases has no effect on dosage compensation (Fig. 3).
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FIG. 3. The dosage compensation of endogenous X-linked genes is not affected by RNAi-mediated depletion of H3K4me3, H3K36me3, or H3K36me2. S2 cells were treated with dSet1, dSet2, or Mes-4 dsRNA; GFP dsRNA was used as a control. The steady-state levels of G6PD, PGD, and SPT6 were determined by real-time RT-PCR and corrected for the level of RP49 transcripts. The GFP control results are set at a value of 1, and an abrogation of dosage compensation would result in a decrease in the level of the three X-linked transcripts below this level. Such an effect is evident when RNAi is used to deplete the cells of the MSL complex by using dsRNA homologous to MSL2 (top panel, gray columns); SPT4 and GPDH are autosomal gene products whose levels are not affected by MSL2 RNAi.
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Implications for targeting of the MSL complex and putative histone deacetylases. As mentioned previously, the MSL complex normally forms on the X chromosome at the site of transcription of the roX genes and spreads by binding to numerous sites for which it has an entire range of affinities; it also binds to activated X-linked genes and enhances their rate of transcription in order to achieve dosage compensation. To date, the mechanism responsible for targeting of the complex to active genes is not understood. In yeast, methylated H3K36 recruits the histone deacetylase (HDAC) complex Rpd3S via the chromodomain of one of its subunits, Eaf3 (4, 9, 11). Eaf3 is a member of the MRG15/MSL3 family, leading to the thought that the MSL complex may be recruited to active genes via the chromodomain of MSL3. The data discussed in the previous section do not support this possibility, at least with regard to the specific methyl marks tested.
Yet, these same data may provide some circumstantial evidence for the recruitment of an HDAC activity to activated genes via the H3K36 methyl mark. As can be seen in Fig. 2B and C, the relative levels of firefly luciferase produced by the roX-bearing and control plasmids following SET2 and MES-4 RNAi are higher than those in the GFP knockdowns. This result could be explained by the failure to recruit an HDAC. The increase in the level of firefly luciferase produced by the roX-bearing plasmid is greater than the increase produced by the control plasmid. The reason for this difference in response of the two reporter genes is likely to be attributable to the enhanced acetylation of the roX-bearing compensated plasmid: while the acetylation marks characteristic of activated promoters should be present at comparable levels on FF and roX-FF plasmids, the chromatin of the latter is highly enriched in H4K16ac (Fig. 1E).
Possible mechanisms of transcriptional enhancement by H4K16ac. Covalent modifications such as lysine acetylation and serine phosphorylation alter the charge differential between histones and DNA, thereby reducing the strength of their association and, at least in theory, facilitating the disassembly and removal of nucleosomes by the elongating RNAP II complex. A second mechanism of action of H4K16ac has been suggested by the discovery of an acidic patch formed by an H2A/H2B dimer with which the basic tail of histone H4 from a neighboring nucleosome can associate (6, 14). In reconstituted nucleosomal arrays, the acetylation of H4 at lysine 16 prevents the conversion of the array into a 30-nm fiber thought to represent a level of compaction unfavorable to transcription (23). The MSL complex may achieve the enhancement in the rate of transcription responsible for dosage compensation by either or both of these effects.
This research was supported by grant GM15691 from the National Institutes of Health.
Published ahead of print on 17 September 2007. ![]()
Supplemental material for this article may be found at http://mcb.asm.org/. ![]()
Present address: Cancer Research Center of Hawaii, Honolulu, HI 96813. ![]()
Present address: Stowers Institute for Medical Research, Kansas City, MO 64110. ![]()
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